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Feb 11, 2005 | In vitro diagnostic microarrays are an important tool in oncology.

While much has been made of the potential for genomics to drive the process of drug discovery, the impact of genomics on medicine and human health is appearing first in molecular diagnostics, particularly in the area of cancer detection and monitoring.

In December, the FDA granted regulatory clearance to the Affymetrix GeneChip System 3000Dx (GCS 3000Dx), an instrumentation system to analyze in vitro diagnostic (IVD) microarrays. This is the first microarray instrument to be cleared by the FDA for IVD use, providing a standardized platform for nucleic acid diagnostics.

Affymetrix can now offer its diagnostic partners an FDA-cleared system to develop and commercialize diagnostic assays, such as Roche Diagnostics' AmpliChip CYP450 test that is currently offered in the European Union. The FDA clearance of the Affymetrix GCS 3000Dx follows the August ISO certification of the instrument and array manufacturing facilities and the September IVD CE marking of the instrument system in the EU.

The clearance will facilitate the "Powered by Affymetrix" program whereby Affymetrix partners with developers of genotyping and gene-expression diagnostics that can now be performed on the GCS 3000Dx system. Under the program, Affymetrix provides technology and expertise for products that are developed, branded, and marketed by the diagnostic partners — such as Veridex LLC. Affymetrix has recently granted this Johnson & Johnson company long-term, comprehensive access to its GeneChip technology to create and market in vitro diagnostics for cancer. According to Robert Lipshutz, senior vice president of molecular diagnostics and emerging markets at Veridex, microarrays are an important new tool in clinical oncology.


SPOT ON: GCS 3000Dx's accurate gridding and consistent scanner-to-scanner performance helped it win FDA approval for IVD use.
Microarray-based tests have already hit the market. The Molecular Profiling Institute (MPI) recently announced that it is the sole provider in the United States for MammaPrint, a prognostic test developed by Agendia that helps identify how a breast cancer patient's tumor will behave. MPI, in collaboration with the Netherlands-based Agendia, and AmeriPath, will offer MammaPrint through physician referral to breast cancer patients nationwide beginning this year.

MPI was formed in late 2003 by the Translational Genomics Research Institute and the International Genomics Consortium, and was designed to be a specialty reference laboratory that utilizes discoveries from the Human Genome Project to analyze cancers from individual patients. MPI's first molecular profile program, Target Now, was launched in September 2003 and is designed for cancer patients for whom all standard therapies have failed. Patients can have their cancer sampled, profiled, and assessed to determine if one or more drug targets can be identified in their tumor tissue.


Toward Personal Medicine 
MammaPrint employs gene-expression profiling to assess the recurrence risk in breast cancer patients. Oncologists receive detailed prognostic information on women with primary invasive breast cancer aged 55 years or younger who are lymph-node negative with either a positive or negative estrogen receptor status. This test may provide valuable assistance for oncologists in formulating tailor-made treatment plans.

Tests based on proteomic technology are also being developed. The National Cancer Institute (NCI) announced last December that Science Applications International Corporation-Frederick Inc. has made two-year awards totaling $13.4 million to two research teams to develop blood tests that can detect the earliest signs of cancer and other diseases.

Scientists from Fred Hutchinson Cancer Research Center, in Seattle, and the University of Michigan Medical School, in Ann Arbor, will lead the teams. Collaborating institutions include the Institute for Systems Biology, in Seattle; Pacific Northwest National Laboratory, in Richland, Wash.; and the Plasma Proteome Institute, in Washington, D.C. The initial aim of the NCI-funded consortium is to identify serum biomarkers whose expression is altered in people with cancer or who are at high risk of developing the disease. The consortium's ultimate goal is to create biomarker-based blood tests that can identify the onset and risk of a wide range of cancers and other diseases so they can be prevented or treated at the earliest possible stage.* 

Robert M. Frederickson is a biotech writer based in Seattle. E-mail: rfreder@yahoo.com. 





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